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© Research
Publication : RNA (New York, N.Y.)

FISH-quant v2: a scalable and modular tool for smFISH image analysis.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in RNA (New York, N.Y.) - 28 Mar 2022

Imbert A, Ouyang W, Safieddine A, Coleno E, Zimmer C, Bertrand E, Walter T, Mueller F,

Link to Pubmed [PMID] – 35347070

Link to DOI – 10.1261/rna.079073.121

RNA 2022 06; 28(6): 786-795

Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression and its regulatory mechanisms. Today, these methods are applicable at a large scale, which in turn come with a need for adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular tool accessible for both experts and non-experts. Our user-friendly package allows the user to segment nuclei and cells, detect isolated RNAs, decompose dense RNA clusters, quantify RNA localization patterns and visualize these results both at the single-cell level and variations within the cell population. This tool was validated and applied on large-scale smFISH image data sets, revealing diverse subcellular RNA localization patterns and a surprisingly high degree of cell-to-cell heterogeneity.

https://pubmed.ncbi.nlm.nih.gov/35347070